Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008072.1 Corchorus capsularis cultivar CVL-1 contig08093, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 71874
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:973 original size:22 final size:22
Alignment explanation
Indices: 948--989 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
938 GGGATTACAA
948 TTGA-CCCCAACCCGGGACCCAG
1 TTGACCCCCAA-CCGGGACCCAG
970 TTGACCCCCAACCGGGACCC
1 TTGACCCCCAACCGGGACCC
990 GGTTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (22 bp):
TTGACCCCCAACCGGGACCCAG
Found at i:4327 original size:64 final size:64
Alignment explanation
Indices: 4270--4441 Score: 206
Period size: 64 Copynumber: 2.7 Consensus size: 64
4260 CCGCCCTACT
4270 AGGGCGGCTCGCA-ACGGATC-AACCGCCCAGCT-GGGACGGCTTCATCTTGTGAGGCCGCCCCT
1 AGGGCGG-TCGCAGACGG-TCAAACCGCCC-GCTGGGGACGGCTTCATCTTGTGAGGCCGCCCCT
4332 TG
63 TG
** * * *
4334 AGGGCGGTTTCAGATGGTCAAACCGTCCTCTGGGGACGGCTTCATCTTGTGAGGCCGCCCCTTG
1 AGGGCGGTCGCAGACGGTCAAACCGCCCGCTGGGGACGGCTTCATCTTGTGAGGCCGCCCCTTG
** * * *
4398 AGGGCGGTTTCAGATGGTCAAACCGTCCTCTGGGGACGGCTTCA
1 AGGGCGGTCGCAGACGGTCAAACCGCCCGCTGGGGACGGCTTCA
4442 CCATTTGAAG
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
63 7 0.07
64 93 0.93
ACGTcount: A:0.16, C:0.30, G:0.33, T:0.22
Consensus pattern (64 bp):
AGGGCGGTCGCAGACGGTCAAACCGCCCGCTGGGGACGGCTTCATCTTGTGAGGCCGCCCCTTG
Found at i:4455 original size:64 final size:64
Alignment explanation
Indices: 4302--4441 Score: 280
Period size: 64 Copynumber: 2.2 Consensus size: 64
4292 CCGCCCAGCT
4302 GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
1 GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
4366 GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
1 GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
4430 GGGACGGCTTCA
1 GGGACGGCTTCA
4442 CCATTTGAAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.14, C:0.28, G:0.34, T:0.24
Consensus pattern (64 bp):
GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
Found at i:4468 original size:64 final size:64
Alignment explanation
Indices: 4302--4471 Score: 189
Period size: 64 Copynumber: 2.7 Consensus size: 64
4292 CCGCCCAGCT
* * * *** *
4302 GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
1 GGGACGGCTTCACCTTGTGAAGCCGCACCACCAAGGCGGTTTCAGATGGTCAAACCGTCCTCTG
* * * *** *
4366 GGGACGGCTTCATCTTGTGAGGCCGCCCCTTGAGGGCGGTTTCAGATGGTCAAACCGTCCTCTG
1 GGGACGGCTTCACCTTGTGAAGCCGCACCACCAAGGCGGTTTCAGATGGTCAAACCGTCCTCTG
*
4430 GGGACGGCTTCACCATT-TGAAGCCGCATCACCAAGGCGGTTT
1 GGGACGGCTTCACC-TTGTGAAGCCGCACCACCAAGGCGGTTT
4472 GAACCGTGGC
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
64 95 0.98
65 2 0.02
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (64 bp):
GGGACGGCTTCACCTTGTGAAGCCGCACCACCAAGGCGGTTTCAGATGGTCAAACCGTCCTCTG
Found at i:5538 original size:23 final size:24
Alignment explanation
Indices: 5506--5556 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
5496 GAGACAATAG
5506 AAAAAGCTCTCACAAAGGAGTCCC
1 AAAAAGCTCTCACAAAGGAGTCCC
*
5530 AAAAA-CTCTCACAAAGGAGTTCC
1 AAAAAGCTCTCACAAAGGAGTCCC
5553 AAAA
1 AAAA
5557 GACAATAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (24 bp):
AAAAAGCTCTCACAAAGGAGTCCC
Found at i:5592 original size:23 final size:23
Alignment explanation
Indices: 5566--5617 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
5556 AGACAATAGA
*
5566 AAAAACTCTCACAAAGGAGTCCC
1 AAAAACTCTCACAAAGAAGTCCC
*
5589 AAAAACTCTCACTAAGAAGTCCC
1 AAAAACTCTCACAAAGAAGTCCC
5612 ATAAAA
1 A-AAAA
5618 GAAACAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.48, C:0.27, G:0.10, T:0.15
Consensus pattern (23 bp):
AAAAACTCTCACAAAGAAGTCCC
Found at i:8899 original size:32 final size:31
Alignment explanation
Indices: 8863--8930 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
8853 TTTAGTAATG
*
8863 ACAATTAAGAAATATGTTTTTAAAAA-AAGGGT
1 ACAATT-AGAAATAT-ATTTTAAAAATAAGGGT
*
8895 ACAATTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTAGAAATATATTTTAAAAATAAGGGT
*
8926 TCAAT
1 ACAAT
8931 CGGAAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.28
31 17 0.53
32 6 0.19
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (31 bp):
ACAATTAGAAATATATTTTAAAAATAAGGGT
Found at i:8916 original size:30 final size:32
Alignment explanation
Indices: 8871--8936 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
8861 TGACAATTAA
* *
8871 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
*
8902 GAAATAT-ATTTTAAAAATAAGGGTTCAATCG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
8933 GAAA
1 GAAA
8937 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGGGTACAATCG
Found at i:19133 original size:11 final size:11
Alignment explanation
Indices: 19086--19127 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
19076 CCTTTTCCTA
*
19086 TATAAAATAAT
1 TATAAATTAAT
19097 TAATCAAA-TAAT
1 T-AT-AAATTAAT
19109 TATAAATTAAT
1 TATAAATTAAT
19120 TATAAATT
1 TATAAATT
19128 TGTTATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 15 0.54
12 7 0.25
13 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:39750 original size:21 final size:22
Alignment explanation
Indices: 39711--40020 Score: 109
Period size: 22 Copynumber: 14.3 Consensus size: 22
39701 CGATGATAAG
39711 AATATTTCATAGGGAGGTTACC
1 AATATTTCATAGGGAGGTTACC
* * *
39733 AATA-TTCATAGTGTGGTTATCAA
1 AATATTTCATAGGGAGGTTA-C-C
* *
39756 AAAATTTCAT-TGGA---TACC
1 AATATTTCATAGGGAGGTTACC
* *
39774 AAAATTTCATA-GGAAGTTACC
1 AATATTTCATAGGGAGGTTACC
* ** *
39795 AAAATTTTGT-GAGGAGGCTACCC
1 AATATTTCATAG-GGAGGTTA-CC
*
39818 AA-ATTTCATGGGGAGGTTACC
1 AATATTTCATAGGGAGGTTACC
* * * * *
39839 AAAATTTCATAAGAAAGTTGCC
1 AATATTTCATAGGGAGGTTACC
***
39861 AATATTTCATAGGGTCCTTACC
1 AATATTTCATAGGGAGGTTACC
* *
39883 AAAATTTTATAGGGAGGTT-CC
1 AATATTTCATAGGGAGGTTACC
* * ** *
39904 AAAATTTAATA-TCATGGTTATC
1 AATATTTCATAGGGA-GGTTACC
* * * ** *
39926 AAAATTTCATTGGAAATTTTCC
1 AATATTTCATAGGGAGGTTACC
* * * *
39948 AAAATTTCATAAGAATGTTACC
1 AATATTTCATAGGGAGGTTACC
* *
39970 AAAATTTTATAGGGAGGTTACC
1 AATATTTCATAGGGAGGTTACC
* ** *
39992 AAAATTTCATAAAGAGATTACC
1 AATATTTCATAGGGAGGTTACC
*
40014 AAAATTT
1 AATATTT
40021 GATATGGACG
Statistics
Matches: 216, Mismatches: 57, Indels: 30
0.71 0.19 0.10
Matches are distributed among these distances:
18 13 0.06
19 1 0.00
20 3 0.01
21 45 0.21
22 139 0.64
23 10 0.05
24 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (22 bp):
AATATTTCATAGGGAGGTTACC
Found at i:39862 original size:22 final size:22
Alignment explanation
Indices: 39770--40195 Score: 194
Period size: 22 Copynumber: 19.7 Consensus size: 22
39760 TTTCATTGGA
39770 TACCAAAATTTCATAGG-AAGT
1 TACCAAAATTTCATAGGAAAGT
** * *
39791 TACCAAAATTTTGTGAGG-AGGC
1 TACCAAAATTTCAT-AGGAAAGT
* * * *
39813 TACCCAAATTTCATGGGGAGGT
1 TACCAAAATTTCATAGGAAAGT
*
39835 TACCAAAATTTCATAAGAAAGT
1 TACCAAAATTTCATAGGAAAGT
* * ****
39857 TGCCAATATTTCATAGGGTCCT
1 TACCAAAATTTCATAGGAAAGT
* * *
39879 TACCAAAATTTTATAGGGAGGT
1 TACCAAAATTTCATAGGAAAGT
* ** **
39901 T-CCAAAATTTAATATCATGGT
1 TACCAAAATTTCATAGGAAAGT
* * *
39922 TATCAAAATTTCATTGGAAATT
1 TACCAAAATTTCATAGGAAAGT
* * *
39944 TTCCAAAATTTCATAAGAATGT
1 TACCAAAATTTCATAGGAAAGT
* * *
39966 TACCAAAATTTTATAGGGAGGT
1 TACCAAAATTTCATAGGAAAGT
39988 TACCAAAATTTCATA--AAGAGAT
1 TACCAAAATTTCATAGGAA-AG-T
* *
40010 TACCAAAATTTGATATGG-ACGT
1 TACCAAAATTTCATA-GGAAAGT
* * * *
40032 TAACAAAGTTTCTTAAG-AAGT
1 TACCAAAATTTCATAGGAAAGT
* *
40053 TACC---ATTCCATAAGG-AGGT
1 TACCAAAATTTCAT-AGGAAAGT
* * **
40072 TATCAAAATTTTATAGGCTAGT
1 TACCAAAATTTCATAGGAAAGT
** * *
40094 TACTGAAATTTCATAGGTAACT
1 TACCAAAATTTCATAGGAAAGT
* **
40116 TACCGAAATTTCATAAAAAAGT
1 TACCAAAATTTCATAGGAAAGT
** *
40138 TTTCAAATTTTCATAGGAAAGT
1 TACCAAAATTTCATAGGAAAGT
* *
40160 TACCAGAATTTCA-ATGG-AGGT
1 TACCAAAATTTCATA-GGAAAGT
*
40181 TACCAAAATGTCATA
1 TACCAAAATTTCATA
40196 TGGGGTGACT
Statistics
Matches: 292, Mismatches: 98, Indels: 29
0.70 0.23 0.07
Matches are distributed among these distances:
18 4 0.01
19 8 0.03
20 1 0.00
21 56 0.19
22 221 0.76
23 1 0.00
24 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
TACCAAAATTTCATAGGAAAGT
Found at i:39923 original size:87 final size:88
Alignment explanation
Indices: 39772--39998 Score: 230
Period size: 87 Copynumber: 2.6 Consensus size: 88
39762 TCATTGGATA
* * * * * * ***
39772 CCAAAATTTCATAGGAA-GTTACCAAAATTTTGT-GAGGAGGCTACCCAAATTTCATGGGGA-GG
1 CCAAAATTTCATAAGAATCTTACCAAAATTTTATAG-GGAGGTTACCAAAATTTAAT-ATCATGG
39834 TTACCAAAATTTCATAAGAAAGTTG
64 TTACCAAAATTTCATAAGAAAGTTG
* **
39859 CCAATATTTCAT-AGGGTCCTTACCAAAATTTTATAGGGAGGTT-CCAAAATTTAATATCATGGT
1 CCAAAATTTCATAAGAAT-CTTACCAAAATTTTATAGGGAGGTTACCAAAATTTAATATCATGGT
* ** * *
39922 TATCAAAATTTCATTGGAAATTTT
65 TACCAAAATTTCATAAGAAAGTTG
*
39946 CCAAAATTTCATAAGAATGTTACCAAAATTTTATAGGGAGGTTACCAAAATTT
1 CCAAAATTTCATAAGAATCTTACCAAAATTTTATAGGGAGGTTACCAAAATTT
39999 CATAAAGAGA
Statistics
Matches: 113, Mismatches: 21, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
86 2 0.02
87 78 0.69
88 32 0.28
89 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (88 bp):
CCAAAATTTCATAAGAATCTTACCAAAATTTTATAGGGAGGTTACCAAAATTTAATATCATGGTT
ACCAAAATTTCATAAGAAAGTTG
Found at i:40562 original size:48 final size:48
Alignment explanation
Indices: 40406--40562 Score: 147
Period size: 48 Copynumber: 3.3 Consensus size: 48
40396 CCCGAAAGGT
** * *
40406 AAAGGTTATTTATCACGGCCATCG-GGAGCCAAAAAAGTCGCAGATGCC
1 AAAGGTTATCCATCACAGCCATCGAGG-GCCAAAAAAGTCACAGATGCC
* * * *
40454 AAAGGTTATCCATCACAGCCATCGAGGGCCATAAACGGCAC-GAAAGCC
1 AAAGGTTATCCATCACAGCCATCGAGGGCCAAAAAAGTCACAG-ATGCC
* * * * *
40502 AAAGGTTTTCCATCATAGCCATTGAGGGCCAAAAATGTCCCAGATGCC
1 AAAGGTTATCCATCACAGCCATCGAGGGCCAAAAAAGTCACAGATGCC
* *
40550 TAAGGATATCCAT
1 AAAGGTTATCCAT
40563 TACATCCACC
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
47 1 0.01
48 83 0.95
49 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (48 bp):
AAAGGTTATCCATCACAGCCATCGAGGGCCAAAAAAGTCACAGATGCC
Found at i:53969 original size:10 final size:10
Alignment explanation
Indices: 53933--53980 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
53923 TTAAACAGAC
53933 AAGCTTAATT
1 AAGCTTAATT
53943 AA-CTTAATT
1 AAGCTTAATT
*
53952 ATA-TTTAATT
1 A-AGCTTAATT
*
53962 AAGCTTAATC
1 AAGCTTAATT
53972 AAGCTTAAT
1 AAGCTTAAT
53981 GATTAATAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (10 bp):
AAGCTTAATT
Found at i:55095 original size:6 final size:6
Alignment explanation
Indices: 55084--55110 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55074 ACAAAGGCAA
55084 TGATAT TGATAT TGATAT TGATAT TGA
1 TGATAT TGATAT TGATAT TGATAT TGA
55111 AATCATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
TGATAT
Found at i:69370 original size:2 final size:2
Alignment explanation
Indices: 69363--69389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69353 ATATTTGTGG
69363 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
69390 CCATGGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69472 original size:16 final size:16
Alignment explanation
Indices: 69451--69483 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
69441 CTGTCTTGTC
69451 TAACTTTGACTTCACT
1 TAACTTTGACTTCACT
69467 TAACTTTGACTTCACT
1 TAACTTTGACTTCACT
69483 T
1 T
69484 CCATTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TAACTTTGACTTCACT
Found at i:71865 original size:31 final size:31
Alignment explanation
Indices: 71796--71865 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
71786 TCCTTTTGTG
*
71796 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCACGTGCCACTTTTTGAAA
* * **
71827 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGCCACTTTTTGAAA
71858 CACGTGGC
1 CACGTGGC
71866 GTGACATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGCCACTTTTTGAAA
Done.